The compliance with standards calls for proper designed EMI filters. EMI typically comprises common mode (cm) and differential mode (dm) noise. A systematic optimization of EMI filters requires the knowledge of the contribution and distribution of these two noise sources. The paper discusses different methods that allow the independent measurement of cm and dm noise. One suitable method described in detail integrates the separation set-up into the Line Impedance Stabilization Network (LISN). However, a correct interpretation of the measured results requires a characterization of the unavoidable modal conversion of the complete set-up - i.e. the measured level at the dm output in case of pure cm excitation and vice versa. As shown in this paper, the implementation of a standard LISN introduces a high amount of imperfections causing the undesired modal conversion. Thus, for the first time, this paper describes the characterization of the whole set-up including the LISN.